From 1130d3b258023013f0987c057d5d7805c2f9748f Mon Sep 17 00:00:00 2001 From: Jonathan Berrisch Date: Mon, 25 Sep 2023 11:05:27 +0200 Subject: [PATCH 1/9] Add threeparttable latex package --- package_lists/latex_packages.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/package_lists/latex_packages.txt b/package_lists/latex_packages.txt index a8fb2de..ddc93f3 100644 --- a/package_lists/latex_packages.txt +++ b/package_lists/latex_packages.txt @@ -108,3 +108,4 @@ xkeyval xpatch xstring zref +threeparttablex \ No newline at end of file From 5e3fb88021060c9a22ad0075e7f29505434763aa Mon Sep 17 00:00:00 2001 From: Jonathan Berrisch Date: Tue, 26 Sep 2023 13:01:18 +0200 Subject: [PATCH 2/9] Add gdb for cpp debugging --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index abec9b1..5e9e163 100644 --- a/Dockerfile +++ b/Dockerfile @@ -39,6 +39,7 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele zsh \ gnupg2 \ nano \ + gdb \ ssh-client \ fontconfig \ ttf-mscorefonts-installer \ From 407fee29ec1756629a7e5891e5f8ab6a95179707 Mon Sep 17 00:00:00 2001 From: Jonathan Berrisch Date: Wed, 27 Sep 2023 10:22:12 +0200 Subject: [PATCH 3/9] Add nbformat python package --- .devcontainer/devcontainer.json | 1 + package_lists/latex_packages.txt | 2 +- package_lists/python_packages.txt | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 0be3964..5ba99f7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -34,6 +34,7 @@ "ms-python.python", "ms-python.black-formatter", "visualstudioexptteam.vscodeintellicode", + "ms-toolsai.jupyter", // R "REditorSupport.r", "rdebugger.r-debugger", diff --git a/package_lists/latex_packages.txt b/package_lists/latex_packages.txt index ddc93f3..72f657f 100644 --- a/package_lists/latex_packages.txt +++ b/package_lists/latex_packages.txt @@ -96,6 +96,7 @@ texdoc # Package Documentation textcase textpos threeparttable +threeparttablex thumbpdf #! To find packages: tlmgr search --global --file "authblk.sty" tracklang @@ -108,4 +109,3 @@ xkeyval xpatch xstring zref -threeparttablex \ No newline at end of file diff --git a/package_lists/python_packages.txt b/package_lists/python_packages.txt index f392db0..a18572b 100644 --- a/package_lists/python_packages.txt +++ b/package_lists/python_packages.txt @@ -14,6 +14,7 @@ Jinja2 kaleido matplotlib meteostat +nbformat numdifftools numpy pandas From 5f567a3b9b5d941057b2fc0f2a4f65564868a197 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 16:07:28 +0000 Subject: [PATCH 4/9] Bump ubuntu from `ec050c3` to `aabed32` Bumps ubuntu from `ec050c3` to `aabed32`. --- updated-dependencies: - dependency-name: ubuntu dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5e9e163..e053a48 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:jammy@sha256:ec050c32e4a6085b423d36ecd025c0d3ff00c38ab93a3d71a460ff1c44fa6d77 +FROM ubuntu:jammy@sha256:aabed3296a3d45cede1dc866a24476c4d7e093aa806263c27ddaadbdce3c1054 SHELL ["/bin/bash", "-c"] From d2877442304904fd65a33e3e3310a07979ea3429 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 16:37:25 +0000 Subject: [PATCH 5/9] Bump docker/setup-buildx-action from 2 to 3 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build_deploy_dev.yml | 2 +- .github/workflows/build_deploy_master.yml | 2 +- .github/workflows/build_deploy_size.yml | 2 +- .github/workflows/build_on_pr.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_deploy_dev.yml b/.github/workflows/build_deploy_dev.yml index 6232204..aeb2375 100644 --- a/.github/workflows/build_deploy_dev.yml +++ b/.github/workflows/build_deploy_dev.yml @@ -17,7 +17,7 @@ jobs: uses: actions/checkout@v3 - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 with: install: true - diff --git a/.github/workflows/build_deploy_master.yml b/.github/workflows/build_deploy_master.yml index 34089e2..cecb51c 100644 --- a/.github/workflows/build_deploy_master.yml +++ b/.github/workflows/build_deploy_master.yml @@ -17,7 +17,7 @@ jobs: uses: actions/checkout@v3 - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 with: install: true - diff --git a/.github/workflows/build_deploy_size.yml b/.github/workflows/build_deploy_size.yml index 49cdaa3..f63e313 100644 --- a/.github/workflows/build_deploy_size.yml +++ b/.github/workflows/build_deploy_size.yml @@ -17,7 +17,7 @@ jobs: uses: actions/checkout@v3 - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 with: install: true - diff --git a/.github/workflows/build_on_pr.yml b/.github/workflows/build_on_pr.yml index 4d6c9fb..8b4b278 100644 --- a/.github/workflows/build_on_pr.yml +++ b/.github/workflows/build_on_pr.yml @@ -16,7 +16,7 @@ jobs: uses: actions/checkout@v3 - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 with: install: true - From 7ff8e7a18b9c8afa862e681123f52dd12308e425 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 16:37:29 +0000 Subject: [PATCH 6/9] Bump docker/login-action from 2 to 3 Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build_deploy_dev.yml | 2 +- .github/workflows/build_deploy_master.yml | 2 +- .github/workflows/build_deploy_size.yml | 2 +- .github/workflows/build_on_pr.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_deploy_dev.yml b/.github/workflows/build_deploy_dev.yml index 6232204..172918b 100644 --- a/.github/workflows/build_deploy_dev.yml +++ b/.github/workflows/build_deploy_dev.yml @@ -22,7 +22,7 @@ jobs: install: true - name: Login to GitHub Container Registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} diff --git a/.github/workflows/build_deploy_master.yml b/.github/workflows/build_deploy_master.yml index 34089e2..43b9156 100644 --- a/.github/workflows/build_deploy_master.yml +++ b/.github/workflows/build_deploy_master.yml @@ -22,7 +22,7 @@ jobs: install: true - name: Login to GitHub Container Registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} diff --git a/.github/workflows/build_deploy_size.yml b/.github/workflows/build_deploy_size.yml index 49cdaa3..5420a0c 100644 --- a/.github/workflows/build_deploy_size.yml +++ b/.github/workflows/build_deploy_size.yml @@ -22,7 +22,7 @@ jobs: install: true - name: Login to GitHub Container Registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} diff --git a/.github/workflows/build_on_pr.yml b/.github/workflows/build_on_pr.yml index 4d6c9fb..03ca816 100644 --- a/.github/workflows/build_on_pr.yml +++ b/.github/workflows/build_on_pr.yml @@ -21,7 +21,7 @@ jobs: install: true - name: Login to GitHub Container Registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} From 954f1f8f540489ed5150f70481dd2a1c5b7d7d89 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 16:37:33 +0000 Subject: [PATCH 7/9] Bump docker/build-push-action from 4 to 5 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v4...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build_deploy_dev.yml | 2 +- .github/workflows/build_deploy_master.yml | 2 +- .github/workflows/build_deploy_size.yml | 2 +- .github/workflows/build_on_pr.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_deploy_dev.yml b/.github/workflows/build_deploy_dev.yml index 6232204..29fc029 100644 --- a/.github/workflows/build_deploy_dev.yml +++ b/.github/workflows/build_deploy_dev.yml @@ -36,7 +36,7 @@ jobs: echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV - name: Build and push - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v5 with: context: . push: true diff --git a/.github/workflows/build_deploy_master.yml b/.github/workflows/build_deploy_master.yml index 34089e2..2d78235 100644 --- a/.github/workflows/build_deploy_master.yml +++ b/.github/workflows/build_deploy_master.yml @@ -36,7 +36,7 @@ jobs: echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV - name: Build and push - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v5 with: context: . push: true diff --git a/.github/workflows/build_deploy_size.yml b/.github/workflows/build_deploy_size.yml index 49cdaa3..de1a19f 100644 --- a/.github/workflows/build_deploy_size.yml +++ b/.github/workflows/build_deploy_size.yml @@ -35,7 +35,7 @@ jobs: echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV - name: Build and push - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v5 with: context: . push: true diff --git a/.github/workflows/build_on_pr.yml b/.github/workflows/build_on_pr.yml index 4d6c9fb..bc3b38f 100644 --- a/.github/workflows/build_on_pr.yml +++ b/.github/workflows/build_on_pr.yml @@ -34,7 +34,7 @@ jobs: echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV - name: Build and push - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v5 with: context: . push: true From caa2a6cd181fdcb7facb8d80d3c65db7660f9631 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 16:37:37 +0000 Subject: [PATCH 8/9] Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build_deploy_dev.yml | 2 +- .github/workflows/build_deploy_master.yml | 2 +- .github/workflows/build_deploy_size.yml | 2 +- .github/workflows/build_on_pr.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_deploy_dev.yml b/.github/workflows/build_deploy_dev.yml index 6232204..db03663 100644 --- a/.github/workflows/build_deploy_dev.yml +++ b/.github/workflows/build_deploy_dev.yml @@ -14,7 +14,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v2 diff --git a/.github/workflows/build_deploy_master.yml b/.github/workflows/build_deploy_master.yml index 34089e2..c4f1850 100644 --- a/.github/workflows/build_deploy_master.yml +++ b/.github/workflows/build_deploy_master.yml @@ -14,7 +14,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v2 diff --git a/.github/workflows/build_deploy_size.yml b/.github/workflows/build_deploy_size.yml index 49cdaa3..8b7c6a1 100644 --- a/.github/workflows/build_deploy_size.yml +++ b/.github/workflows/build_deploy_size.yml @@ -14,7 +14,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v2 diff --git a/.github/workflows/build_on_pr.yml b/.github/workflows/build_on_pr.yml index 4d6c9fb..99f7a84 100644 --- a/.github/workflows/build_on_pr.yml +++ b/.github/workflows/build_on_pr.yml @@ -13,7 +13,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v2 From d0c944012754fa25f4931a4667bf0a87a3acbc92 Mon Sep 17 00:00:00 2001 From: Jonathan Berrisch Date: Thu, 5 Oct 2023 09:34:45 +0200 Subject: [PATCH 9/9] Update RSPM snapshot --- Dockerfile | 4 ++-- package_lists/r_packages.txt | 1 + package_lists/r_packages_github.txt | 1 - 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index e053a48..e317c10 100644 --- a/Dockerfile +++ b/Dockerfile @@ -117,8 +117,8 @@ ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}" ENV R_VERSION=4.3.1 # Set RSPM snapshot see: -# https://packagemanager.rstudio.com/client/#/repos/1/overview -ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2023-08-28 +# https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2023-10-04&distribution=ubuntu-22.04 +ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-04 COPY install_scripts/install_r.sh /install_scripts/install_r.sh COPY package_lists/r_packages.txt /package_lists/r_packages.txt diff --git a/package_lists/r_packages.txt b/package_lists/r_packages.txt index de2c4f7..060a2cd 100644 --- a/package_lists/r_packages.txt +++ b/package_lists/r_packages.txt @@ -112,5 +112,6 @@ tsrobprep VineCopula wiqid xaringan +xaringanExtra xtable zoo diff --git a/package_lists/r_packages_github.txt b/package_lists/r_packages_github.txt index 72464d1..11adf38 100644 --- a/package_lists/r_packages_github.txt +++ b/package_lists/r_packages_github.txt @@ -1,5 +1,4 @@ BerriJ/strsplit.fix -gadenbuie/xaringanExtra@*release GreenGrassBlueOcean/RefinitivR ManuelHentschel/vscDebugger@*release stenevang/sftp